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diff test-data/report.html @ 0:f848a7f97332 draft

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"planemo upload commit fadaff2d55736bf8c580541d6089c83cd4106a1f"
author iuc
date Thu, 31 Oct 2019 19:40:40 -0400
parents
children 82fb5e3bb93e
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report.html	Thu Oct 31 19:40:40 2019 -0400
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+<!DOCTYPE html
+PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
+<html>
+<head>
+<title>smallest :: BRESEQ :: Mutation Predictions</title>
+<style type = "text/css">
+body {font-family: sans-serif; font-size: 11pt;}
+th {background-color: rgb(0,0,0); color: rgb(255,255,255);}
+table {background-color: rgb(1,0,0); color: rgb(0,0,0);}
+tr {background-color: rgb(255,255,255);}
+.mutation_in_codon {color:red; text-decoration : underline;}
+.snp_type_synonymous{color:green;}
+.snp_type_nonsynonymous{color:blue;}
+.snp_type_nonsense{color:red;}
+.mutation_header_row {background-color: rgb(0,130,0);}
+.read_alignment_header_row {background-color: rgb(255,0,0);}
+.missing_coverage_header_row {background-color: rgb(0,100,100);}
+.new_junction_header_row {background-color: rgb(0,0,155);}
+.copy_number_header_row {background-color: rgb(153,102,0);}
+.alternate_table_row_0 {background-color: rgb(255,255,255);}
+.alternate_table_row_1 {background-color: rgb(235,235,235);}
+.gray_table_row {background-color: rgb(230,230,245);}
+.polymorphism_table_row {background-color: rgb(160,255,160);}
+.highlight_table_row {background-color: rgb(192,255,255);}
+.reject_table_row {background-color: rgb(255,200,165);}
+.user_defined_table_row {background-color: rgb(255,255,0);}
+.information_table_row {background-color: rgb(200,255,255);}
+.junction_repeat {background-color: rgb(255,165,0)}
+.junction_gene {}
+.hidden { display: none; }
+.unhidden { display: block; }
+
+</style>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+<script type="text/javascript">
+  function hideTog(divID) {
+    var item = document.getElementById(divID);
+    if (item) {
+      item.className=(item.className=='hidden')?'unhidden':'hidden';
+    }
+  }
+  function showTog(butID) {
+    var button = document.getElementById(butID);
+    if (button) {
+      button.value=(button.value=='Show')?'Hide':'Show';
+    }
+  }
+</script>
+
+</head>
+<body>
+<table width="100%" border="0" cellspacing="0" cellpadding="3">
+<tr>
+<td><a href="http://barricklab.org/breseq"><img src="evidence/breseq_small.png" /></a></td>
+<td width="100%">
+<b><i>breseq</i></b>&nbsp;&nbsp;version 0.34.0&nbsp;&nbsp;
+<br><a href="index.html">mutation predictions</a> | 
+<a href="marginal.html">marginal predictions</a> | 
+<a href="summary.html">summary statistics</a> | 
+<a href="output.gd">genome diff</a> | 
+<a href="log.txt">command line log</a>
+</td></tr></table>
+
+<p>
+<!--Mutation Predictions -->
+<p>
+<!--Output Html_Mutation_Table_String-->
+<table border="0" cellspacing="1" cellpadding="3">
+<tr><th colspan="6" align="left" class="mutation_header_row">Predicted mutations</th></tr><tr>
+<th>evidence</th>
+<th>position</th>
+<th>mutation</th>
+<th>annotation</th>
+<th>gene</th>
+<th width="100%">description</th>
+</tr>
+
+<!-- Item Lines -->
+
+<!-- Print The Table Row -->
+<tr class="normal_table_row">
+<td align="center"><a href="evidence/JC_11.html">JC</a></td><!-- Evidence -->
+<td align="right">41,405</td><!-- Position -->
+<td align="center">(GCG)<sub>2&rarr;5</sub></td><!-- Cell Mutation -->
+<td align="center">coding&nbsp;(325/873&nbsp;nt)</td>
+<td align="center"><i>NinC</i>&nbsp;&rarr;</td>
+<td align="left">NinC protein</td>
+</tr>
+<!-- End Table Row -->
+
+<!-- Print The Table Row -->
+<tr class="normal_table_row">
+<td align="center"><a href="evidence/MC_PLOT_8.html">MC</a>&nbsp;<a href="evidence/JC_12.html">JC</a></td><!-- Evidence -->
+<td align="right">41,601</td><!-- Position -->
+<td align="center">(AAC)<sub>2&rarr;1</sub></td><!-- Cell Mutation -->
+<td align="center">coding&nbsp;(521&#8209;523/873&nbsp;nt)</td>
+<td align="center"><i>NinC</i>&nbsp;&rarr;</td>
+<td align="left">NinC protein</td>
+</tr>
+<!-- End Table Row -->
+
+<!-- Print The Table Row -->
+<tr class="normal_table_row">
+<td align="center"><a href="evidence/JC_13.html">JC</a></td><!-- Evidence -->
+<td align="right">41,716</td><!-- Position -->
+<td align="center">(T)<sub>5&rarr;9</sub></td><!-- Cell Mutation -->
+<td align="center">coding&nbsp;(636/873&nbsp;nt)</td>
+<td align="center"><i>NinC</i>&nbsp;&rarr;</td>
+<td align="left">NinC protein</td>
+</tr>
+<!-- End Table Row -->
+
+<!-- Print The Table Row -->
+<tr class="normal_table_row">
+<td align="center"><a href="evidence/MC_PLOT_9.html">MC</a>&nbsp;<a href="evidence/JC_14.html">JC</a></td><!-- Evidence -->
+<td align="right">44,075</td><!-- Position -->
+<td align="center">(CAAA)<sub>2&rarr;1</sub></td><!-- Cell Mutation -->
+<td align="center">coding&nbsp;(190&#8209;193/624&nbsp;nt)</td>
+<td align="center"><i>Q</i>&nbsp;&rarr;</td>
+<td align="left">late gene regulator</td>
+</tr>
+<!-- End Table Row -->
+
+<!-- Print The Table Row -->
+<tr class="normal_table_row">
+<td align="center"><a href="evidence/SNP_5.html">RA</a></td><!-- Evidence -->
+<td align="right">47,317</td><!-- Position -->
+<td align="center">N&rarr;T</td><!-- Cell Mutation -->
+<td align="center"><span style="white-space: nowrap"><font class="snp_type_nonsynonymous">?87I</font>&nbsp;(<font class="mutation_in_codon">N</font>TC&rarr;<font class="mutation_in_codon">A</font>TC)&nbsp;</span></td>
+<td align="center"><i>lambdap78</i>&nbsp;&larr;</td>
+<td align="left">putative envelope protein</td>
+</tr>
+<!-- End Table Row -->
+</table>
+<p>
+<table border="0" cellspacing="1" cellpadding="3" width="100%">
+<tr><th colspan="11" align="left" class="missing_coverage_header_row">Unassigned missing coverage evidence</th></tr>
+<tr><th>&nbsp;</th><th>&nbsp;</th><th>&nbsp;</th><th>seq&nbsp;id</th>
+<th>start</th>
+<th>end</th>
+<th>size</th>
+<th>&larr;reads</th>
+<th>reads&rarr;</th>
+<th>gene</th>
+<th width="100%">description</th>
+</tr>
+<tr>
+<td><a href="evidence/MC_SIDE_1_7.html">*</a></td>
+<td><a href="evidence/MC_SIDE_2_7.html">*</a></td>
+<td><a href="evidence/MC_PLOT_7.html">&divide;</a></td>
+<td>NC_001416</td>
+<td align="right">1</td>
+<td align="right">38810</td>
+<td align="right">38810</td>
+<td align="center">NA&nbsp;[0]</td>
+<td align="center">[10]&nbsp;13</td>
+<td align="center"><i>nu1&#8211;[O]</i></td>
+<td align="left">nu1,A,W,B,C,nu3,D,E,Fi,Fii,Z,U,V,G,T,H,M,L,K,I,J,lom,orf&#8209;401,orf206b,orf&#8209;314,orf&#8209;194,ea47,ea31,ea59,int,xis,lambdap35,ea8.5,ea22,orf61,orf63,orf60a,exo,bet,gam,kil,cIII,ea10,ral,orf28,lambdap48,N,rexb,rexa,cI,cro,cII,[O]</td>
+</tr>
+<tr>
+<td><a href="evidence/MC_SIDE_1_10.html">*</a></td>
+<td><a href="evidence/MC_SIDE_2_10.html">*</a></td>
+<td><a href="evidence/MC_PLOT_10.html">&divide;</a></td>
+<td>NC_001416</td>
+<td align="right">48475</td>
+<td align="right">48502</td>
+<td align="right">28</td>
+<td align="center">12&nbsp;[10]</td>
+<td align="center">[0]&nbsp;NA</td>
+<td align="center"><i>lambdap79/&#8211;</i></td>
+<td align="left">hypothetical protein/&#8211;</td>
+</tr>
+</table>
+</body></html>
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